riboPicker Files

riboPicker
==========

Identification and removal of rRNA-like sequences using a modified version of
BWA-SW (http://ribopicker.sourceforge.net).

For more information about BWA-SW go to http://bio-bwa.sourceforge.net/

To test the program, please read README_test.txt


SETUP
-----

1. Create the databases used for rRNA screening

   Use command:
      bwaXXX index -p database_name fasta_file_with_rrna_references >out.txt 2>&1 &

      ("XXX" should be replaced by "MAC" or "64" based on your system architecture)

      For alternative system architectures, download BWA version 0.5.9 source
      code from http://bio-bwa.sourceforge.net/
      (http://sourceforge.net/projects/bio-bwa/files/bwa-0.5.9.tar.bz2/download);
      extract the file with "tar -xjf bwa-0.5.9.tar.bz2"; replace files in the
      extracted BWA directory with the files in bwasw_modified_source
      (distributed with riboPicker); run "make" in the BWA directory.

   Notes:   (i) It is advised to remove very short or long sequences from files
                retrieved from public resources. Most likely, those sequences
                are a result of misannotations and should not be included in the
                database.
           (ii) Removing duplicates may reduce the database size and speed up
                analysis. Tools such as PRINSEQ (http://prinseq.sourceforge.net/)
                can assist with this task.
          (iii) There seem to be some issues with Mac OSX 10.6.8 that will
                require you to compile the program (the bwaMAC version might
                crash).
           (iv) The non-redundant rRNA database can be downloaded from: 
                http://edwards.sdsu.edu/ribopicker/rrnadb/

2. Change values in riboPickerConfig.pm (if applicable)
   DB_DIR
   PROG_NAME
   PROG_DIR
   DBS
   DBS_DEFAULT

   Notes: (i) If the bwaXXX program is located in the same directory as the
              ribopicker.pl file, please specify ./ as program directory (use
              constant PROG_DIR => './';).


USAGE
-----

Run as:
   perl ribopicker.pl [options] -f <file> -dbs <list> ...

or rename file and set chmod +x to run as:
   ./ribopicker [options] -f <file> -dbs <list> ...

Try 'ribopicker -h' for more information on the options.


DEPENDENCIES
------------

The PERL script requires these other modules:

   riboPickerConfig  (included)
   Data::Dumper
   Getopt::Long
   Pod::Usage
   File::Path      >= 2.07
   Cwd
   FindBin

   Note: If you do not like to use FindBin, replace the FindBin module with either of:

   A File::Basename + Cwd version:
   use File::Basename qw(dirname);
   use Cwd qw(abs_path);
   use lib dirname(abs_path($0));

   A File::Basename + File::Spec version:
   use File::Basename qw(dirname);
   use File::Spec;
   use lib dirname(File::Spec->rel2abs($0));


BUG REPORTS
-----------

If you find a bug please email me at <rschmieder_at_gmail_dot_com> or 
report a bug at http://sourceforge.net/p/ribopicker/bugs/ so that I can
make riboPicker better.


COPYRIGHT AND LICENSE
---------------------

Copyright (C) 2011  Robert SCHMIEDER

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with
this program.  If not, see <http://www.gnu.org/licenses/>.


VERSION HISTORY
---------------

(If not otherwise stated, changes apply to the standalone and web version after
version 0.3.)

ribopicker-0.4.3:
Extended documentation and help. Added example data to the standalone version.

ribopicker-0.4.2:
Added FindBin (and alternatives) to standalone version to prevent issues when
runnning the tool from a different directory.

ribopicker-0.4.1:
Extended the input format from ACGTN to full nucleic acid ambiguity code
(ACGTURYKMSWBDHVNX-). Added FASTQ input support (standalone).

ribopicker-0.4:
Allow to filter results by alignment length in addition to the coverage and
identity thresholds.

ribopicker-0.3:
Enhanced interface with additional information of results (domain and phyla by
database). Extended FAQ and Manual sites on sourceforge. Added and updated
databases.
With release 0.3, riboPicker is now available as standalone version for offline
use and/or integration into your processing pipeline.

ribopicker-0.2:
Added coverage plot generation that allows plot updating based on current
threshold values. Added coverage values output file to output selection.

ribopicker-0.1:
First public release of riboPicker.